Background: Although minimally invasive surgery (MIS) affords several advantages compared to conventional open surgery, robotic MIS systems still have many limitations. One of the limitations is the non-uniform gripping force due to mechanical strings of the existing systems. To overcome this limitation, a surgical instrument with a pneumatic gripping system consisting of a compressor, catheter balloon, micro motor, and other parts is developed. Method: This study aims to implement a surgical instrument with a pneumatic gripping system and pitching/yawing joints using micro motors and without mechanical strings based on the surgical-operation-by-wire (SOBW) concept. A 6-axis external arm for increasing degrees of freedom (DOFs) is integrated with the surgical instrument using LabVIEW® for laparoscopic procedures. The gripping force is measured over a wide range of pressures and compared with the simulated ideal step function. Furthermore, a kinematic analysis is conducted. To validate and evaluate the system’s clinical applicability, a simple peg task experiment and workspace identification experiment are performed with five novice volunteers using the fundamentals of laparoscopic surgery (FLS) board kit. The master interface of the proposed system employs the hands-on-throttle-and-stick (HOTAS) controller used in aerospace engineering. To develop an improved HOTAS (iHOTAS) controller, 6-axis force/torque sensor was integrated in the special housing. Results: The mean gripping force (after 1,000 repetitions) at a pressure of 0.3 MPa was measured to be 5.8 N. The reaction time was found to be 0.4 s, which is almost real-time. All novice volunteers could complete the simple peg task within a mean time of 176 s, and none of them exceeded the 300 s cut-off time. The system’s workspace was calculated to be 11,157.0 cm3. Conclusions: The proposed pneumatic gripping system provides a force consistent with that of other robotic MIS systems. It provides near real-time control. It is more durable than the existing other surgical robot systems. Its workspace is sufficient for clinical surgery. Therefore, the proposed system is expected to be widely used for laparoscopic robotic surgery. This research using iHOTAS will be applied to the tactile force feedback system for surgeon’s safe operation.